if you dont have a protective casing for the fishing rod. i.e. cause the length etc.

You can always face the heavy end (butt) of the fishing rod to the front of the car, (minus the reel), as being the heavier end it be less likely to break when driving along tracks with heavy overgrowth. Also I find tying the rod to the centre of the roof rack can minimize the chance of it being caught in overhead branches.